During the assembly and examination of sets of reference post-source decay (PSD) time-of-flight mass spectral data for glycolipids, oligosaccharides and their derivatives, we noted patterns in the small but nevertheless significant calibration errors. Investigation of the sources of these errors led to detailed review of the software implemented by the manufacturer, which had been based on the theoretical and experimental studies of Hillenkamp et al. during the design and testing of the prototype for the commercial Vision 2000 RTOF instrument. These studies brought to light hidden parameters that were instrument-dependent and also showed that there were some errors in the software coding. A new protocol for PSD spectra calibration has been developed, based on the original studies carried out in M(nster and a clear improvement in the mass assignment accuracy has been achieved. The new procedures are being shared with the manufacturer and with other users of reflectron TOF instruments, especially those in the Vision 2000 series.